For each BAM, we use samtools to retrieve the reads in the region(s)) of interest. The reads are then filtered with samjs (https://github.com/lindenb/jvarkit/wiki/SamJS) to only keep the reads carrying an intron-exon junction at the desired location(s). Basically, the javascript-based filter loops over the CIGAR string of the read, computes the genomic interval skipped when the cigar operator is a deletion or a skipped region/intron. The read is printed if it describes the new intron-exon junction.